Modified makefile to work for gcc version 4.5.3 or higher

diff --git a/README.md b/README.md
index 836a3677770e79db7b571e4fb2542d648986a165..6e8acd8fb2df0f100fc6a0622bde5467aa8b649a 100644 (file)
--- a/README.md
+++ b/README.md
@@ -121,7 +121,7 @@ If your file does not satisfy the requirements, you can use
 'convert-sam-for-rsem' to convert it into a BAM file which RSEM can
 process. Please run
  
 'convert-sam-for-rsem' to convert it into a BAM file which RSEM can
 process. Please run
  

-   convert-sam-for-rsem --help
+    convert-sam-for-rsem --help

 
 to get usage information or visit the [convert-sam-for-rsem
 documentation
 
 to get usage information or visit the [convert-sam-for-rsem
 documentation

diff --git a/makefile b/makefile
index 900a8b3d3a7d47db5cc29ada4e1c78fb08d38b64..e2711b532be12b82ff45a01d845597c0ed8d0ff8 100644 (file)
--- a/makefile
+++ b/makefile
@@ -54,7 +54,7 @@ rsem-parse-alignments : parseIt.o sam/libbam.a
        $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz 
 
 parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
        $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz 
 
 parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp

-       $(CC) $(COFLAGS) parseIt.cpp
+       $(CC) -Wall -O2 -c -I. parseIt.cpp

 
 
 rsem-build-read-index : utils.h buildReadIndex.cpp
 
 
 rsem-build-read-index : utils.h buildReadIndex.cpp


@@ -132,10 +132,10 @@ rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
 
 rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
        $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -o $@
 
 rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
        $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -o $@

-       
+

 rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
        $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -o $@
 rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
        $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -o $@

-       
+

 clean:
        rm -f *.o *~ $(PROGRAMS)
        cd sam ; ${MAKE} clean
 clean:
        rm -f *.o *~ $(PROGRAMS)
        cd sam ; ${MAKE} clean